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Pathology Tumor Detection#296

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Nic-Ma merged 8 commits intoProject-MONAI:masterfrom
bhashemian:camelyon_ignite
Aug 2, 2021
Merged

Pathology Tumor Detection#296
Nic-Ma merged 8 commits intoProject-MONAI:masterfrom
bhashemian:camelyon_ignite

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@bhashemian bhashemian commented Aug 1, 2021

Description

This PR adds a pathology pipeline example to train and evaluate a model to detect tumors on whole-slide histopathology images. This pipeline uses ignite-based MONAI workflow.

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@bhashemian bhashemian changed the title Pathology Pathology Tumor Detection Aug 1, 2021
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bhashemian commented Aug 1, 2021

@wyli, @Nic-Ma, it would be great if either of you can review and merge this PR. Thanks.

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Nic-Ma commented Aug 1, 2021

Hi @drbeh ,

Thanks for the quick PR!
I think the dataset_subset.json is too long in the code base, could you please help put it in our google drive storage? And use MONAI download API to download it in this example?
@wyli , what do you think?

Thanks.

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wyli commented Aug 1, 2021

yes, the current shared drive at https://drive.google.com/drive/u/2/folders/1ZOqwF44newvq-jOSgnbXRDWRD9DRq8hH

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bhashemian commented Aug 1, 2021

Sure, let me check that.

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Update default dataset
be2a247 
Signed-off-by: Behrooz <[email protected]>
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bhashemian commented Aug 1, 2021 •
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@Nic-Ma, @wyli, I moved the datasets to the google drive and updated the README with the download links. For testing this pipeline (without any performance gain), you should download two images (tumor_001 and tumor_101) as mentioned in the README from here
You also need the dataset_0_subset_0.json from here.

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wyli commented Aug 1, 2021

Looks good to me. My concern is that we'll probably break this tutorial when developing the core codebase. This happened before Project-MONAI/MONAI#2571, and it was detected manually -- which is not efficient.

So I'm wondering whether we should also convert this into an integration test in MONAI (e.g. https://github.com/Project-MONAI/MONAI/blob/dev/tests/test_integration_determinism.py), to download some testing data (e.g. https://github.com/Project-MONAI/MONAI/blob/7f42efe0ab55730c302aba87bcd9bf75c4bfc496/tests/test_patch_wsi_dataset.py#L27-L28), run a few training steps.

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bhashemian commented Aug 1, 2021

@wyli, I agree with you that we should have an integration test in MONAI for pathology too. I can make a simplified version of this for integration but it requires to download two large images (3.1GB and 1.4GB). Wouldn't it be a problem?

Anyways, We should have some examples in tutorials, shouldn't we?

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wyli commented Aug 1, 2021

Adding tests will be great. gigabytes of testing data will cause issues, is it possible to have a smaller test?

Yes we should have examples in the tutorial, and ideally other developers should be able to help maintain it when you are not available.

@wyli wyli mentioned this pull request Aug 1, 2021
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thanks, created a separate ticket for the integration test Project-MONAI/MONAI#2676. @Nic-Ma could you please help confirm/merge this PR?

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Looks good to me.
Could you please help also update the README doc of this repo to include this pipeline?
https://github.com/Project-MONAI/tutorials/blob/master/README.md

Thanks in advance.

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Update READMEs
fe7c6b3 
Signed-off-by: Behrooz <[email protected]>
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bhashemian commented Aug 2, 2021

README is updated!

@Nic-Ma Nic-Ma merged commit b3130b6 into Project-MONAI:master Aug 2, 2021
@bhashemian bhashemian deleted the camelyon_ignite branch August 2, 2021 15:39
boneseva pushed a commit to boneseva/MONAI-tutorials that referenced this pull request Apr 21, 2024
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Pathology Tumor Detection (Project-MONAI#296)
592eff6 
* Add README

Signed-off-by: Behrooz <[email protected]>

* Add camelyon train/evaluate pipline with ignite

Signed-off-by: Behrooz <[email protected]>

* Update default dataset

Signed-off-by: Behrooz <[email protected]>

* Update README with dataset downloads

Signed-off-by: Behrooz <[email protected]>

* Change the reference to the default dataset

Signed-off-by: Behrooz <[email protected]>

* Update READMEs

Signed-off-by: Behrooz <[email protected]>
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